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A bioimage informatics platform for high-throughput embryo phenotyping

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to promi...

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Autores principales: Brown, James M, Horner, Neil R, Lawson, Thomas N, Fiegel, Tanja, Greenaway, Simon, Morgan, Hugh, Ring, Natalie, Santos, Luis, Sneddon, Duncan, Teboul, Lydia, Vibert, Jennifer, Yaikhom, Gagarine, Westerberg, Henrik, Mallon, Ann-Marie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862285/
https://www.ncbi.nlm.nih.gov/pubmed/27742664
http://dx.doi.org/10.1093/bib/bbw101
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author Brown, James M
Horner, Neil R
Lawson, Thomas N
Fiegel, Tanja
Greenaway, Simon
Morgan, Hugh
Ring, Natalie
Santos, Luis
Sneddon, Duncan
Teboul, Lydia
Vibert, Jennifer
Yaikhom, Gagarine
Westerberg, Henrik
Mallon, Ann-Marie
author_facet Brown, James M
Horner, Neil R
Lawson, Thomas N
Fiegel, Tanja
Greenaway, Simon
Morgan, Hugh
Ring, Natalie
Santos, Luis
Sneddon, Duncan
Teboul, Lydia
Vibert, Jennifer
Yaikhom, Gagarine
Westerberg, Henrik
Mallon, Ann-Marie
author_sort Brown, James M
collection PubMed
description High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest.
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spelling pubmed-58622852018-07-10 A bioimage informatics platform for high-throughput embryo phenotyping Brown, James M Horner, Neil R Lawson, Thomas N Fiegel, Tanja Greenaway, Simon Morgan, Hugh Ring, Natalie Santos, Luis Sneddon, Duncan Teboul, Lydia Vibert, Jennifer Yaikhom, Gagarine Westerberg, Henrik Mallon, Ann-Marie Brief Bioinform Papers High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest. Oxford University Press 2016-10-14 /pmc/articles/PMC5862285/ /pubmed/27742664 http://dx.doi.org/10.1093/bib/bbw101 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Papers
Brown, James M
Horner, Neil R
Lawson, Thomas N
Fiegel, Tanja
Greenaway, Simon
Morgan, Hugh
Ring, Natalie
Santos, Luis
Sneddon, Duncan
Teboul, Lydia
Vibert, Jennifer
Yaikhom, Gagarine
Westerberg, Henrik
Mallon, Ann-Marie
A bioimage informatics platform for high-throughput embryo phenotyping
title A bioimage informatics platform for high-throughput embryo phenotyping
title_full A bioimage informatics platform for high-throughput embryo phenotyping
title_fullStr A bioimage informatics platform for high-throughput embryo phenotyping
title_full_unstemmed A bioimage informatics platform for high-throughput embryo phenotyping
title_short A bioimage informatics platform for high-throughput embryo phenotyping
title_sort bioimage informatics platform for high-throughput embryo phenotyping
topic Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862285/
https://www.ncbi.nlm.nih.gov/pubmed/27742664
http://dx.doi.org/10.1093/bib/bbw101
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